Amy Pond: The 12th Doctor
by Thunderstrike16
Summary: AU: The Doctor has Regenerated after Trenzalore and with interesting results. How would she take it and what adventures will she go with Clara and others. No romance between the Doctor and Clara for obvious reasons.
1. Prologue: A Familiar Face

**This is an idea I had when I was at school and started writing it. Don't get me wrong, I really like Peter Capaldi's work as the 12** **th** **Doctor and I'm not happy that the next season will be in early 2017. This may or may not be one-shot but I'll see if I decide to make it into a multi-chapter.**

 **Hope you like it and please check out my other Fanfics, including, The Jedi through Time and Space, a Doctor Who and Star Wars crossover.**

 **I don't own anything, only OC's and made up locations.**

 **Enjoy!**

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 **A Familiar Face**

Clara walked into the Console Room of the TARDIS, she last saw The Doctor go into the TARDIS after regaining another Regeneration Cycle and defeating the Daleks. The room of was empty and she looked at the console to see one of The Doctor's bowls of Fish Finger's and Custard on the console.

She didn't bother to think of how long that was there but she soon noticed his clothes were on the ground. She internally shuttered at the thought of him being naked again, her looksee wasn't that bad the first time but it just shocked her and made her blush to see him like that without a care in the world.

But he was old and wrinkly now and she didn't want that image in her head. She started walking down a flight of steps when she heard footsteps behind her. She turned around and gasped a little at seeing The Doctor.

He was back to his old, joyful and youthful self and it made her smile.

She sighed in relief and had big smile plastered on her face, "Doctor."

"Hello." He said with a small, tired smile.

"You're young again. Your ok. You didn't even change your face." She said in a relieved tone.

The Doctor let out a chuckle and said," It started. I can't stop it now, this is just a reset. A whole new Regeneration Cycle. Oh!"

The Doctor picked up the bowl of food and proceeded to eat it and placed it back on the console.

"Taking a bit longer. Just breaking it in."

The Doctor worked the console and proceeded to put it in flight but groaned in pain. He knew he had a limited time left, but he just needed to hold it for just a few more minutes.

"It all just disappears, does it? Everything just are, gone in a moment, like breaking in a mirror. Any moment now, he's a-coming."

"Who's coming?" Clara asked.

"The Doctor."

Clara knew this was going but she didn't want The Doctor change," But, you, you are The Doctor.

"Yep, and I always will be." He said.

He soon felt some sort of energy forming and knew it was coming. He looked at his hands sadly as they began to glow with Regeneration Energy.

"But time change, and so must I."

The Doctor soon heard giggling and caught a glimpse of child wearing winter clothing run past him and up the stairs.

"Amelia." The Doctor said with a shocked expression.

Clara looked around confused but found no one. She then looked at The Doctor, who looked like he saw a ghost.

"Who's Amelia?"

A small fond smile formed on The Doctor's face and said," The first face, this face saw."

The Doctor looked at his hands, had a look of realization and said," We all change. When you think about it, we are all different people. All through our lives. But that's ok, that's good, you gotta keep on moving. So long as you, remember, all the people, you used to be. I will not forget, one line of this. Not one day, I swear, I will always remember, when The Doctor was me."

Clara felt like crying, she didn't want to lose The Doctor, even though he would be fine, just another person. But she knew she must accept it and The Doctor already had.

The Doctor heard footsteps coming down the stairs and looked, with a shocked expression to see Amy walk down the stairs.

He knew he was hallucinating; Amelia was in 1930's New York with Rory. But deep down he just wanted to see her again, she was and always will be a great friend, another being in the family he has loved and cherished over the centuries. He will never forget her.

'Amy' came down the steps and stopped right in front of The Doctor and she smiled. He did too, even in his imagination she was still the loving and caring woman he had the pleasure to travel with.

'Amy' placed her hand on The Doctor's cheek, he did the same. She smiled and said.

"Raggedy Man… goodnight."

The Doctor blinked and she was gone. He noticed the Regeneration Energy on his hands were starting to intensify.

It was time.

He took off his bowtie and let it fall to the floor.

"I hope the next one will have a liking to Bowties, and be ginger." He mused to himself.

"No, no, no, no. Please don't change." Clara said on the verge of tears and held out her hand.

The smiled at his Impossible Girl one last time and was about to hold her hand in comfort but then… BOOM!

He was covered with Regeneration energy, his head snapped up, his hands out and he felt himself changing. It hurt and soon heard screaming of sorts but he couldn't tell if it was him or Clara. But it soon started to sound a little high pitched but the process soon died down and he was panting.

In a state of shock, he snapped his head at Clara, who had a look of shock and confusion. He walked over to her and looked her straight in the eyes, but soon reeled in pain and held the side where his Kidney's were located.

"Kidney's! I got new Kidney's! I don't like the color." He said.

"O- of your Kidney's?" Clara asked in a state of shock.

He shook his head and noticed his hair, it was long, it sorta reminded him of his 8th self. And it was also… Ginger.

"Yes." He whispered.

"What?" Clara asked.

"Ha! Ha! Ginger! After 11 or how some view it 13 bodies! Ginger! I'm finally Ginger!" he cried happily!"

He kissed his hair and hugged Clara who shrieked in surprise and he kissed her head and let her go.

"Although it is a little long. What does the rest of look like… ooo, Scottish accent as well. And I'm a tiny bit shorter than my last body. Well?" He asked Clara.

Clara got of her shock but she didn't know how to explain on was happening.

"Uh, well… this will come as a little bit of a shock." Clara managed to say.

The Doctor had a curious look and said," Why's that?"

Clara looked around for a mirror and found a full length one the TARDIS placed behind The Doctor and she silently thanked her.

"Look behind you."

The Doctor turned around and gasped. He was a she, and she looked exactly like Amy, except she was wearing his clothes. The irony was that it looked raggedy and she would've found it funny if she was not currently mad.

If was an attempt of a joke, she didn't find it funny or liked it one bit.

"Very funny dear. You give me a mirror that makes look like Amelia! Jokes over, show me what I really look like. Clara?" She asked with annoyed tone.

"It's not a trick."

"What?"

It's not a trick."

"What?!"

Before The Doctor or Clara could say anything else, the TARDIS lurched and shook with The Doctor running to the console.

"OH We're crashing!"

Into what?!"

"Just stay calm! Also, one question. You know how to fly this thing?" The Doctor asked.

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 **Hope you guys liked it. If I do decide to go along with this I'll make a Day of the Doctor chapter and she can meet her previous selves. Also I added a little to the chapter.**


	2. Chapter 1: Crash and Faint

**I've decided to continue this! Hope you guys like this and tell me how I'm doing.**

 **I own nothing.**

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 **Chapter 1**

River Song was with her Grandfather, Brian Williams, who was Rory's father. She was having one of her visits with him and it always made her wonder what would happen if she would've had a normal or somewhat normal life if she wasn't taken by the Silence and Madame Kovarian to become a weapon against The Doctor. But she couldn't because changing the timeline would be disastrous.

But as usual, someone's attempt to defeat The Doctor was quickly taken care of with The Doctor victorious. That was one of the reasons why she loved him. For Brian it had been a year since Amy and Rory had been sent back to 1930's New York. While for her, she wasn't sure and for The Doctor, who knew how long, but she knew by now he would have Clara Oswald as a companion.

That was the issue with her meeting The Doctor in different points in her and his life. Spoilers everywhere and she had to be careful but, she always loved the look of annoyance when she said it.

It was also a matter of time before she would meet The Doctor final time and she would have to face her death at the Library. Knowing about one's own personal future was rough but if it meant keeping the Universe intact and the man you love alive, it was worth it.

Also it was only a matter of time before she would meet the one Regeneration The Doctor would feel most guilty about.

Right now, she was telling him a story about one her Archeological Digs, which involved stealing an artifact from a tomb that was considered sacred by the locals. When she was about to tell him about when she teleported away from the locals once she did steal it. A familiar sound echoed in the vicinity.

 _Vrroomp. Vrroomp. Vrroomp. Crash!_

"His driving still needs work." River muttered.

"Do you remember that from your travels?" Brian asked.

"Can't say granddad. But let's go see what he has done."

They went outside and found the TARDIS had crashed into the yard and had inadvertenly destroyed a Bird Bath and some flowers, Brian had planted a couple of weeks ago.

"I just installed that thing a couple of weeks ago and the flowers are mess. I'm guessing this is one of his 'entrances' you told me about?" Brian asked.

"Yes granddad, it was. Let's see if he's al-"

Before she could finish, the doors opened and the last person they would see look out of the TARDIS.

Amy.

She looked around and ran out of the TARDIS. She was in The Doctor's clothes, all tattered and she when she saw them, she smiled.

"Look, familiar faces and a destroyed yard… yikes. Brian, you really need to do some yard work and River, my River, new me and I'm ginger. And I might be hallucinating but your house is smaller on the outside, Brian." 'Amy' said and continued babbling.

Brian was confused on what was happening but he had broke out of it for a second when he thought Rory was in there as well. River on the other hand, she knew what was going on and internally sighed and felt sorry for her husband or wife now for what's to come.

Clara came out of the TARDIS, disheveled and saw The Doctor running around the yard and talking. She noticed a man and River looking shocked and not surprised.

River noticed Clara and said," You must be Clara, I take it The Doctor has changed?"

Clara had a confused look and said," Yeah, River, we met, remember… oh wait, different version of you, timeline was?"

River smirked and said, "Yes and don't reveal too much, spoilers."

"Right." The school teacher said.

She remembered The Doctor had told her about the adventures he had with River. And how it all had sounded confusing to her.

"Are you one of his companions? If so, is my son Rory in there? And where is The Doctor?" Brian asked.

Clara pointed at 'Amy' and said," That's The Doctor right there."

The Doctor must've heard her because she went over to her and said," Clara! There you are! Quick, we need to find out who destroyed Brian's yard and why I'm dressed like this."

"Doctor, you need to calm down and also, you destroyed his yard and your wearing the same clothes you've been wearing for who knows, how long." Clara explained.

"Really Well that's solved then… Everyone! Take five!" She said and promptly passed out on the ground.

River ran to her and said to the others," Help me take her into the house. Brian, get a hot towel ready."

"But I thought Amy was stuck in the past, Anthony told me-"

"We'll or I'll explain it to you later. Clara, help me." River said and got The Doctor's shoulders while Clara got her legs.

Brian led them into the house and went to get a hot towel while other two got The Doctor onto the couch. River checked The Doctor to see if she was injured in anyway and Clara decided to lighten the mood.

"You know, he or she is still married to you." She said and attempted to laugh.

River glared at her and that silenced Clara.

"Sorry."

"Quite alright, so I take it you just came from Trenzalore?"

"Yeah, quite an interesting experience. I wasn't there for the whole thing but just part of it. He does talk about you sometimes. All good things."

River smiled with a hint of mischief and said," I'm going to have to thank him for talking about me next time I see him in his previous self."

Clara went bright red and said," Please, leave that kind of talk when you are with The Doctor, and not me."

"Well… no promises." River said with a wink and Clara blushed brighter.

The Doctor's mouth opened and golden Regeneration energy flowed out of her mouth and disappeared.

"Wow, never seen that before." Clara said in awe.

"That's normal for a Time Lord, regeneration could be tricky for a few and a lottery." River said.

"I think he or she told me that before… this isn't going to be easy." Clara said.

"It never is, you just have to push on." River said.

Brian came back from the kitchen and gave River the towel and she placed it on The Doctor's head. He had also brought a pair of woman's pajamas as well.

"Where did you get those?" Clara asked.

"I have a box of old clothes that were from Rory and Amy, haven't gotten the chance to toss or sell them yet. So… what exactly is going on?" He asked.

"Well, with her species, Time Lords, they have a way of cheating death. When they are close to it, they explode in a way and energy consumes them. And their cells change and rearrange until their someone new. Not only do they change what they look like but also their personalities but, their memories stay intact. Some can choose their own face, The Doctor can't." River explained.

Brian sat in his Recliner with a dazed face and somewhat deep in thought and said," Well, I'm no stranger to the impossible or weird, because of The Doctor but, I think I need time to process this."

"It happens. Clara, can you explain how he may have changed into Amy?"

Clara thought for a second and said," Well, before he changed, he saw a hallucination of Amy but I'm not sure. I'm not even sure if this is the same person.

"She is Clara, she is the same person, but a little bit different. Bearing the face of a lost loved one who you cared deeply about will be hard on her. But, I know she'll get through it with you by her side. River said reassuringly. "Also, let's get these on her." She said and got the pajamas.

"I hope so and alright." Clara said.

She looked at The Doctor, who had a peaceful look on her face. And she wondered.

How will all of this play out?

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 **That's it for this chapter. Next one will deal with the Doctor and her new issues and with some danger. See you next time!**

 **P.S. I fixed the chapter a little.**


	3. Chapter 2: Sorrow and Comfort

**Next chapter is up! This will be an emotional chapter and something interesting at the end.**

 **I own nothing.**

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 **Chapter 2**

After getting The Doctor dressed, Clara found herself in the kitchen with River, while Brian was at the store getting some groceries. Clara had made some coffee for herself and River, River was reading her Journal.

They had also tried to get into the TARDIS but even with their keys she wouldn't open. River then realized that she was remodeling and would let them in later. That's when they decided to go into the kitchen to talk.

Clara wasn't sure how to start the conversation, last time she saw River was during Trenzalore with the Great Intelligence, but she was a ghost or a data ghost. But this time she's seeing the real flesh and blood one. The Doctor had told her about his many encounters with River in random moments of her time stream and started to make sense to her due to her traveling with him.

"So, The Doctor never told me about what happened to Amy and Rory. I saw a glimpse of them when I was in The Doctor's Time Stream. Just what happened… if you want to tell me." She added.

River closed her Journal and sighed," Well, I was there and I know for a fact he didn't tell you. It happened in New York and we just dealt with the Weeping Angels… do you know what they are?"

Clara recalled her first encounter back on her second time on Trenzalore and how she and The Doctor were surrounded by them in the snow. It wasn't fun, nor being naked in the snow, even though The Doctor used holographic clothes or whatever; but she knew what they were.

"Sorta but it's a long story. I take it you know more about them?"

"Yes, they're the oldest beings in the Universe, Quantum-Locked, the only way they could move is when it's either dark or when no is looking. They eat Time Energy or any power source and by touching someone, they send them to a different time period and they feed off the days they would have spent in their original timeline.

Now, after we had dealt them when we were in New York, Rory saw a grave that had his name and that set his fate and he was sent back when a remaining Angel touched him. Amy became very distraught and The Doctor tried to talk her out of going after him. She was always stubborn but she had made up her mind. She said goodbye to him, turned around and was send back with the gravestone next to Rory's had her name on it, leaving The Doctor and I."

Clara wiped a tear from the corner of her eye. The Doctor never really told her what had happened to Amy and Rory or to his other companions. It hurt too much for him and she understood her boundaries when asking about former companions. Even though for her she had seen and sometimes met his companions from her echoes. The Doctor had told her that she wouldn't see any of her echoes memories and if she did, then he said it wouldn't matter because they weren't her and she how he said"The one and only Clara Oswin Oswald". That helped and she did occasionally have flashbacks of sorts on the matter but it wasn't like she had headaches or anything but it was saddening to see herself or whoever the person was to die.

"You knew didn't you? The Doctor told me they were your parents, why didn't you try to save them?"

River sighed and said," Fixed Point, we couldn't do anything without the universe going haywire. Also, The Doctor can't go anywhere near New York during the time period they were sent. It takes centuries until he can even go to that time period in that location."

"Can't he just go to like maybe New Jersey or something and walk there?" Clara asked.

River raised an eyebrow and then thought about it for a second and said," I think it still applies but I'm not sure, you have to him or her yourself when she wakes up."

"I guess that idea is bullocks then. So, what now?"

River got up and said," You'll have to help her through this and be there for her."

"You're going to stay?" Clara asked surprised.

"Sorry duty and work calls, I would tell you but some of it are spoilers." She said the last part with a mischievous smile.

"The Doctor warned me about you saying that. I could tell it eats at him." Clara said with a grin.

"I'll make sure the next time I see him I'll tell him. And something more." River said with wink and disappeared in a flash of light.

Clara was blushing when she said the last part and she was left by herself in the kitchen. She got up and went to the living room where The Doctor was still sleeping off her Regeneration. Clara placed her coffee on the table and gave The Doctor a sympathetic look. She got closer, fixed her pillow and took a look at The Doctor's sleeping form.

"Doctor worry Doctor; we'll get through this together." She soothingly said.

She heard some sounds of machinery and people outside, she didn't see any construction crews outside so she decided to check it out. She got up and walked to the door and opened it. She found people in uniform jogging across the long and was a perimeter of sorts around the front of the house and some were looking at the TARDIS. She recognized them as UNIT and she saw Kate Stewart and her Osgood walking towards her. The last time she had saw them was during the whole Zygon, Time War crisis.

"Ah Clara, nice to see you again, I see The Doctor has made another one of his entrances?" Kate said.

Clara got out closed the door and said," Yeah he has Kate… may I ask what you are doing here?"

"Reports came in saying something about a blue box that crashed into someone's yard and it didn't have to take a genius to know it was The Doctor."

"That happened 15 minutes ago, what took you so long?"

"Another issue was taking our time and we finally got the chance to come here. So, where is he?"

"Weelll… She's sleeping off her Regeneration in the house."

"Huh, my father told about that and… wait, she?" Kate asked, slightly confused.

"Wow." Osgood said.

Clara fought back a groan from all the stuff that had happened for the past couple of hours or however long it has been and said, "Yeah, it's a long story but she did and she now has the face of someone you might know."

Clara then opened the door and let everyone in. She also thought of what Brian would think of all this once he got back, but that was a bridge that would be crossed later. When they got to the couch, Kate was surprised to see Amelia Pond lying down on the couch.

"Well, this is interesting. Alright, I want you to stay and look after The Doctor and TARDIS. It's a miracle that The Doctor's enemies haven't caught wind of this. Osgood, get Malcolm on the line and tell him to scan for anything." Kate ordered.

The UNIT soldiers who were inside nodded and proceeded to secure the house with Osgood went on the phone to relay Kate's orders.

"Do you need anything?" Kate asked.

"No, I'll wait until she wakes up."

"Then we'll be outside then." Kate said and closed the door once she was outside.

Clara sat in a chair and sighed deeply with everything had happened today. She turned on the TV and was about to change the channel when she heard a moan. She looked at The Doctor, who looked like she was staring to wake up.

"Doctor?" Clara hopefully said.

The Doctor didn't open her eyes but said," How long was I out?"

"About a couple of hours, you just missed River. UNIT is outside guarding you and the TARDIS. "

The Doctor finally opened her eyes and tried to get up but went back down when a sharp pain went through her head. She yelped a little and held her head.

"Are you alright?" Clara asked concerned.

"J-just fine, just aftershocks." She said through gritted teeth.

"Do you need anything? I could get-"

"What I need is you to shut up Clara." The Doctor angrily said.

Clara narrowed her eyes and said, I know you're not feeling well but don't bark at me."

The Doctor then started to relax and said," Sorry, Regeneration is tough… wait, where are we and why does it look familiar?" The Doctor said as she looked around.

"We crashed into someone's yard that you know, Brian Williams."

The Doctor had a raised eyebrow and said," Why are we… oh right. So what happened while I was out?"

"River was here and then left, UNIT is outside right now. They came when reports of a blue box started to come in."

The Doctor got up again and sat at the edge of the couch. She looked at herself and frowned.

"Who's clothes are these?"

"There Amy's Pajamas, Brian had a box full of Amy's and Rory's old clothes."

The Doctor's face clouded in confusion again, and Clara guessed she had forgotten she had changed genders and taken on Amy's face when she regenerated.

"Now why would I need…oh." The Doctor realized and her face fell.

Clara had never seen The Doctor so sad and depressed. She had seen The Doctor have her moments before but this one was different.

"Out of the infinite faces in the Universe… I get one my deepest regrets." The Doctor whispered.

"Doctor, things happen for a reason and it's a part of life." Clara said, trying to help.

The Doctor looked at Clara with a pained expression that then turned to anger and said," Part of life?! Clara, I have been to one part of the Universe to the next, witnessed the birth and death of the Universe itself, had 11 faces with number 12 being someone I cared for deeply, the first face I saw when I Regenerated. Who that I might add, I last saw in tears and was about to be sent to the past to the man she loved."

Tears started to form but The Doctor continued," I had known Amelia since she was 7; I was there when she was at her happiest and lowest when I came back for her. I cared for her and Rory, not just because they would be my future in-laws when I married River but I was a part of their family and I loved them. Now, I have a reminder of her, not just in my best and worst memories but her face and body until I Regenerate again. I have lost many people that I considered family over the centuries but those two are the freshest and it was my job to keep them safe but I didn't Clara… I didn't."

The Doctor tears started to flow freely and Clara gave her a hug which The Doctor hugged her back.

Clara had never seen The Doctor like that before, sure she had seen her sad but she always kept to herself and would voice her emotions when needed. But now she had lowered her walls, and was letting all her sorrow out. Clara knew that The Doctor wouldn't feel closure for quite some time but she had seen another side of The Doctor that few had seen.

The Doctor soon calmed down and was sitting with her face her hands, sniffing with tears. Clara gave her box of tissues and put a comforting hand on her shoulder and The Doctor looked up.

"We'll get through this Doctor, I promise you." Clara smiled reassuringly.

The Doctor grinned a little and said," Thanks Clara, I needed that but there is still a small issue."

"What's that?"

The Doctor then had an embarrassed look and looked like she was trying to come up with something and then said," Well… I'm a girl now, and I may now have to wear makeup and women's clothing… can you… help me with that?"

Clara was silent for a second, processing what The Doctor had said. She then burst into laughter with tears forming her eyes a minute later. And she clutched her stomach as soon as the laughter pain came.

"Oi!" The Doctor cried indigently with a blush.

"I-I'm sorry D-Doctor, yes I-I'll help. Oh blimey." Clara said as she calmed down.

The Doctor rolled her eyes and said," Thanks, now lets go talk to Kate and head to the TARDIS." She said and got up.

"Actually Doctor we can't, I tried to open the door but it won't budge."

"Oh... huh, the old girl must be remodeling herself then. Ok, then we should talk to Kate then."

Clara nodded and they both walked to the door and walked outside. But there was a lot more activity outside and Kate was fast walking to them with a concerned look. Clara had noticed Brian was talking to a couple of UNIT personal as well.

"Kate, good to see you again, thanks for the guarding but I'm-"

"That could wait for later Doctor, we have a crisis and we need you."

The Doctor groaned and said," Great, changed the look and already there is a crisis. What's going on?"

"Cybermen Doctor, they're appearing all over London." Kate gravely said.

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 **That's it for that chapter! I hope I got the emotions right and I'm going to use elements from Dark Water and Death in Heaven with a lot of changes. Comment, fav and I hope you liked it.**


	4. Chapter 3: Problems and a new look

**Next chapter is here! Had to do a lot of research on things and it took time. I hope I did ok and enjoy!**

 **I own nothing.**

* * *

 **Chapter 3**

The Doctor let out an annoyed huff and said, "Brilliant, just finished and there's a possible world ending catastrophe. Some things never change. So, what's the situation?"

"Uh, Doctor. Shouldn't you change first? You're in a Nightie." Clara pointed out.

The Doctor waved her off and said," I don't care, I mean, I do care about how I dress but I've done this before. Amy was in her Pajama's in her first official adventure with me and I've done the same when I was 10, you know, skinny boy. Also, I can't access the TARDIS because she's remodeling."

The Doctor then walked over to Osgood and a couple of others who were near a computer and took it. Clara and Kate looked at each other, shrugged and went after her.

"Ok, so you said Cybermen are appearing all around the world?" The Doctor asked while on the laptop.

"Yes, reports were coming in when they started coming out of St. Paul's Cathedral and stood out in the open. From the reports, they still are and people are thinking it's a public attraction. There about 200+ selfies on the Internet and a couple of Social Media Accounts so far."

The Doctor pinched the bridge of her nose in annoyance and said," Like moths to a flame, find something you lot like and all approach. Human's and their ignorance sometimes don't see danger until it's too late."

Clara coughed at the rude comment and The Doctor seemed to notice.

"No offense."

"Some taken Doctor. What can you find?"

"Well, no spaceships in orbit or any cloaking fields in place. No teleportation residue of any kind. Is there any cases you've been working that might have something to do with this?"

"Osgood." Kate said.

"For the past couple of weeks UNIT spies have infiltrated a facility called 3W or how it stands for 'Don't Cremate Me'."

"Ok, what does that mean?"

"Well it's a way of burying the dead but you see the bodies in some special submerged water, with their Internal Organs intact and are put in Metal Exoskeletons. When it was drained they showed Cybermen and they all activated. We don't know who's in charge but we think it's someone named Missy."

"Missy? Doctor, have you ever heard that name?" Clara asked.

"I know a lot of people Clara, you know that. But no, I haven't and I may have found something."

"What is it?" Kate asked.

The Doctor typed in a couple of commands and then had a shocked looked.

"This is impossible." The Doctor whispered.

"What's the matter?" Clara asked.

"Time Lord tech readings from the 3W Facility. It looks like a part of the Matrix."

"Isn't that a name of a movie made in the United States?"

"No short stack the Matrix stores information and someone must have part of it because they have stored people's consciousness's into it, then purge all of their emotions and then downloaded them back into their heads and boom! Instant Cybermen, with no painful conversion process and now, I have reasons to believe that we're now dealing with a Time Lord or Lady."

"Ok that a problem, do you know who it is and how did you figure it out." Kate asked.

"I don't have a clue and I hacked into their Mainframe and into the information hub."

"Ma'am. We have a message from the square where the Cathedral is." A UNIT soldier said.

"What is it and who is it from?" Kate said.

"It's not for you ma'am, it's for The Doctor. She didn't say who she was but she said she knows The Doctor."

That got The Doctor's full attention and said," Well then, let's go meet her and see what she wants. But first, I need to change my look."

"Really Doctor? Now's not that time." Clara said.

"It is Clara because two reasons: 1. I'm not into the whole Nightie thing. And 2. The Old Girl is ready." The Doctor said as she took out a glowing TARDIS key and ran to the TARDIS.

"Doctor, like Clara said. Now's not the time. We have a crisis on our hands and the fate of the world is in our hands." Kate said, slightly irritated.

The Doctor waved them off and said, I can travel through time and we got someone waiting who knows me and possibly how I work."

"That may be true Doctor, but we need to act now, we don't know what the Cybermen have planned nor how many there are." Clara said.

"We'll get to that soon. But first. Sexy, what do you have for me now." She said and unlocked the door with a smile.

"Excuse me. But am I ever going to get my house and yard back." Brian asked.

"You will, once The Doctor leaves, we'll get out of your hair." Kate said.

The Doctor pushed open the doors and gazed at the new TARDIS.

The inside was the same size as the previous one. The Console was slightly raised, with sleek silver, black stripes going up around the console, with a mechanical look with 2 flat screen monitors both movable on two sides. The Time Rotor was incased in glass with the color being red-orange with the same Gallifreyan Writing on the top with a spinning steel. The floor was made of steel and had 4 stair cases leading somewhere with a small spiraling staircase going down to another floor. On the top floor some bookcases, lamps, chairs were added to have a home feel to it.

4 arches like 9 and 10th Doctor's stared in 4 corners and ended at the Time Rotor but were made of steel to give the room a mechanical, industrial look. The arches had holes inside and had the round things around the sides of the TARDIS that were colored blue, red and gold with the gold lighting up. The overall lighting for the TARDIS was brighter that the 11th Doctor's but had a shadow to it. The color of the interior was a light silver like the 11th's as well.

"Love the work you did dear. Very nice." The Doctor said impressed and ran to the top floor into the hallway to find the wardrobe.

Everyone else walked inside and had a look of aw and looked around."

"Impressive, my father always told me it looked smaller." Kate said.

"I prefer the older look, the one that had a joyful feel and look to it." Brian said.

Clara was admiring everything until she noticed someone was missing.

"Doctor? Where are you?" She asked.

"Right here Clara, and I'm ready to find out what's going on." The Doctor said.

Everyone turned around to look at The Doctor in her new outfit.

She had cowboy boots, black jeans with patches on them, a light blue and red blouse, a brown leather jacket that went to her waist like the 9th Doctor's with a pocket watch in one of the pockets and her Sonic in the other. Her hair was in a pony tail, with a TARDIS key hanging around her neck like a necklace, a red scarf with purple fingerless gloves on.

"Now, let's see who we have to deal with." She said with a confident smile.

* * *

 **That's the end. I had to do research on TARDIS consoles, some clothes Amy wore and other's too. I had to plan out by looking up the episodes, Dark Water and Death in Heaven. I hoped you liked it and I recommend looking up fan art for TARDIS interiors because all of them are pretty well done, imaginative and inspired me a little.**

 **Next Chapter will deal with Missy and other things. Can't Say but… Spoilers.**


	5. Chapter 4: Old Enemy and shock

**Took me awhile to finish and here it is! Hope you like it.**

 **P.S. Shoutout to everyone who has Reviewed and gave me advice**

 **I own nothing.**

* * *

 **Chapter 4**

 **Old Enemy and Shock**

"Right then, let's go, Brian, you stay home and stay inside until this is all over. Kate, you have troops at the square?"

"Yes, we have the area surrounded."

"Alright good, let's go meet whoever this person is." The Doctor said and pulled the Lever after Brian had left the TARDIS.

The square at the Cathedral was surrounded by UNIT troops who were keeping an eye on the not moving Cybermen and a women sitting on a bench, who was dressed in a black dress, with white undershirt and tie that a Victorian look to it. She was looking around with a look of boredom but was soon turned into a smile when she heard a familiar sound.

The TARDIS materialized into the Square with the Doctor first out, with Clara, Kate and Osgood following.

"Aahh, looks like someone Regenerated and got my message. Still fighting for the humans I see Doctor?" The woman said and got with a fake smile.

The Doctor rolled her eyes, crossed her arms, gave her a stern look and said," Seems like you are the one who is behind all this, who are you, how do you know me and what is all this?" She said bluntly.

"Come now such harsh words, I get to see you again and this is the welcome I get?" She said while dodging the question.

"Cut the crap, I know you're a Time Lord because you have Time Lord Tech and what is your game with stealing people's consciousness's and putting their bodies into Cybermen?"

"Well that would ruin the fun of it all now would it? Not when I could do this." She said and snapped her fingers.

The Cybermen immediately took off into the air and soon exploded in the sky, leaving a dark cloud forming with a dome roof nearby opening and other Cybermen came out and flew away.

"Doctor what is going on?" Kate asked worriedly.

"91 Cybermen 1 for each major populated area for all of the United Kingdom and around the world. Able to spread their Cyber pollen to every graveyard and turn everyone into Cybermen." The woman said as if it was nothing.

"Alright jokes over! This face I have, I know quite well and I could tell I have some her personality, which also includes anger and other things. Now. Who. Are. You." The Doctor said with anger and confidence.

But on the inside she was terrified.

"We're old friend Doctor, have you forgotten all the fun times we had, The Master and the Doctor?" The Woman said with fake sadness.

The Doctor had a look of pure horror, she didn't want to believe it and said," No, no, it can't be, you died."

"But lived as always also I go by Missy now, short for Mistress." She said with a smile.

The Doctor's horrified face turned stern and said," What is your plan with all of this?"

"Well, if you don't believe me then check every News outlet around the world and you also get to see the big finish."

"I think we heard enough." Kate said and nodded.

A UNIT soldier fired a dart at Missy's neck and she started swaying.

Well that felt nice, let's do it again." She said and passed out with two UNIT personnel supporting her.

"No, no, no, no wait don't! Kate, what are you doing?!" The Doctor asked.

"Don't worry Doctor we have protocols for this and we will question her properly. C'mon, we have to go to a safe location." Kate said and started ordering everyone around.

"I don't know who she was but I think the Doctor could have handled it." Clara defended.

"Thank you Clara. What do you mean a safe location? Where are you-"

Before the Doctor could finish a UNIT soldier fired a syringe into the Doctor's neck.

"What? You Can't, Blimey."

She started swaying and was helped to the ground with Clara checking her. The Doctor was conscious enough to mutter something into Osgood's ear and then passed out.

"What was that for and what did she say?" Clara asked.

"She said to guard the Graveyards." She said.

"Great more problems, don't worry, she'll be fine, another shot will wake her instantly. Come along and don't worry she'll get paid." Kate said and walked away.

"What paid… how much are we talking about?" Clara asked while following Kate and she remembered that the Doctor told her something about working for UNIT for a time.

Osgood was next to her and showed her something on her Tablet. Her eyes widened and said," Dear God she could've bought a whole lot of Bowties, Fezzes and whatever she would like now. That's more than I make… wait, do I get paid as well?" Clara asked along the way.

Meanwhile, in a nearby graveyard, the Cyber Clouds were forming over it, some bystanders was wondering what was going on. It started to rain, around the world the same thing was happening with puddles forming and water moving near Morgues, other Graveyards, and anywhere else bodies were.

* * *

The Doctor felt a sharp pain in her neck for second and her fluttered open with a sharp pain in her head. She wasn't sure it was post Regeneration or waking up like she had but she could hear the distinct sound of a plane engine. She hadn't felt like that since one night with River and some drinking… it felt weird to think of River like that, maybe it was some of Amy's personality that made her think it was weird.

She then heard someone calling her name.

"Doctor? Doctor? Wake up… are you alright?" A familiar voice asked.

"What do you think Clara? I was knocked out and the fate of the world is my hands as usual." The Doctor said irritably and opened her eyes.

Clara gave her an annoyed look. Her previous Doctor never snapped at her like this and she guessed she had to get used to this.

"Yep, you're ok and we're going to board."

"What? Board what?"

"A UNIT plane, don't worry, their loading up the TARDIS right now."

The Doctor looked around and discovered she was strapped to a chair and saw Kate giving instructions to Osgood.

"Kate!" The Doctor yelled over the plane engine noise.

Kate went over to her and gave her a somewhat sympathetic look and said," Apologies Doctor but we have protocols in place when dealing with an Alien Invasion after what has happened and we needed your full cooperation and we had to consider your history.

"'You don't have a future without Clara and me." The Doctor said. "Do you think your father would have done the same?"

"We both know he would. But who is she?" Kate asked while Missy was being loaded on the plane, still unconscious.

"Long story." The Doctor muttered, not wanting to go into detail about her lifelong battle with her once best friend.

"Explain later then, we have the TARDIS being loaded and we're going to be under your orders once we're inside." She said.

After the Doctor was unrestrained she and everyone else went onboard and soon went into a room that was probably an office, with chairs, computers and a long table.

"Not bad not bad at all, could use a little redecorating, so, where are we going?" She said and stuffed her hands into her jacket pockets.

"Nowhere in particular, you're a moving target so we have to keep your location under lock-and-key. The President is onboard." Kate said the last part to the Pilots on her phone.

"Good call, wait President? You're bringing the American's into this? I can live with that, they are a bunch of nice group of blokes." The Doctor said.

"I can agree with that, their men over there aren't half bad looking." Clara said and made some coffee herself.

"Not the United States President but the President of Earth." An Indian Officer said.

"Now who was the poor bloke who got caught into that job?" The Doctor said and sat at the head of the table.

"Due to the protocols and a unanimous decision made by all World Leaders. When a large scale alien invasion is at hand a President is called for, has full control over every Army and you we're the Candidate right for the job." Kate said.

Clara did a spit-take and nearly dropped her coffee with a horrified look, while the Doctor raised an eyebrow.

"Dear God, the power will go to her head and we'll have to be forced to wear Bowties and Fezzes." Clara said in mock horror.

"Oi! Just to let you know I no longer have a thing for Bowties and Fezzes but these boots I have on, these are cool." The Doctor said and shrugged off what Clara did.

"Ok my fear is gone, what am I then?" Clara asked but she didn't see the eye roll from The Doctor.

"Nothing at all, we didn't consider a position when a Doctor had a traveling partner." Kate said.

"You can be a body guard, a bossy, school teacher, who doesn't know a thing about history." The Doctor absentmindedly suggested.

"Ok, you're just one more insult away from me, socking you in your pretty face." Clara threatened.

"Right sorry, new personality, I think I have a mix between my old one, Amy's and a new one."

"This is your Captain speaking. Please prepare for take-off."

After a little while, The Doctor and Clara went to the Cargo hold to talk to Missy again and see if she would be cooperative. But in the back the Doctor mind she knew she would only give her vague answers.

They found Missy still unconscious on the trolley with the TARDIS in the Corner. The Doctor nodded and a soldier injected her with syringe and she woke up.

"Now, how and why are you still alive?" The Doctor asked bluntly and straight to the point.

"You saved me?" Missy said sweetly.

"Nope, myself and my other incarnations saved Gallifrey." The Doctor said.

"They put it in a pocket dimension." Clara added with the Doctor giving her a nod.

"Yes and no, but I know the best part of knowing something you know?" Missy asked with a smirk. "Not telling you one bit." She said with a taunting smile.

The Doctor felt a twinge of anger boiling within her but she felt someone holding her hand and saw it was Clara, who was trying to calm her down and it worked a little.

"Mrs. President, we're ready for you." The Indian Officer said.

"On my way. Sorry but you wanted to rule the world but meh." The Doctor said and left with Clara but stopped to talk to Osgood.

"What are you doing?" She asked.

"Checking The Master's device to see if there's any useful information, so far nothing."

"Wait, how did you know who she was?" The Doctor asked intrigued.

"We have files on her and her time as Harold Saxon, quite a history you two have, even though you were friends."

"Well things happen, and all of it in Time and Space." The Doctor said.

Clara nodded at Osgood and they left. Osgood thought for a second and her eyes widened, realizing she was offered in a way to travel with the Doctor.

After watching a news report and finding out that Cybermen were popping everywhere from anywhere that had dead bodies and how the rainclouds stayed. The Doctor said it was a sort of like pollination like bees would do and how something more was coming.

"You know, being president is not as interesting, I mean the only thing annoying is when someone keeps saluting you. I can only imagine what Romana went through during her Presidency on Gallifrey." The Doctor and looked at a portrait of the Brigadier while holding a flower.

Kate chuckled and said," My father always want a salute from you, it was his big ambition."

"He sounded like a good man." Clara said.

"That he was Clara and all he had to do was ask." The Doctor said and notice the screen to the Cargo hold was static.

"I'll be right back." The Doctor said and left the room with Clara.

When they got to the Cargo hold they found Missy gone and a pile of ash where Osgood was last and the Doctor realized what Missy had done and she felt a pain of guilt, know she could have saved her.

Clara knew what The Doctor was thinking, and she remembered what River had told her about taking care of her. But she was sure because this Doctor was different than her previous one but she didn't want to show it.

"She was a brave one, I'll give're that one." Missy said from and walked from behind the TARDIS casually.

"She didn't deserve to die, you could've let her live." The Doctor seethed and knew the anger was a mix between Amy and her previous self.

"Meh, not important but you want to know what my plan is? It's involves my present to you and may help your current situation." She said.

"What you are doing is immoral and wrong. You don't care for life at all." Clara said with anger in her voice.

"I knew I liked her Doctor, no wonder why I gave her your number. Oops."

"That was you?" The Doctor asked surprised.

"Wait… I remember now, you're the one who said his number was a helpline." Clara said with a look of realization.

Before they could say anything else Kate ran into the room and said," Doctor! The Cybermen have gotten in and the plane is going down."

"I hate to cut this short but we must move along now." Missy said.

Missy held on to a strap while the plane turned sharply. The Doctor and Clara held on to something while watching in horror as Missy pulled the planes hatch and Kate fell out with a scream.

"Oh my God." Clara said horrified.

"Why did you do that?! You didn't have to do that!" The Doctor yelled angrily.

"If it makes you feel better I'm going to miss her too but just for yelling at me I'll be leaving!" Missy said and pulled out a bracelet.

"Alright boys tear the rest of the plane apart! And kill some Frenchmen while you're at it because they are a snooty bunch. Byee!" She said and teleported **.[1]**

"Doctor! I can't hold on!" Clara yelled.

"Try and get to the TARDIS Clara!" The Doctor yelled.

But the TARDIS soon fell out of the plane and so did The Doctor and Clara. They were in a free fall while they witnessed the plane exploding.

"DOCTOR!" Clara screamed.

"C'mon dear you need to save us." The Doctor said.

The doors to the TARDIS opened but they were far away. The Doctor was close to the Clara so she held her hand in comfort but she didn't think it was working that well.

A streak of silver came near them and the next thing they knew they're were in the TARDIS. Clara was to the Doctor's left, she was panting and looked like she was going to cry. The Doctor repaid her for all she had done for her the entire day and held her. Clara sniffs and small sobs were the only sound in the TARDIS and she relaxed after about a couple of minutes.

Clara muttered a thanks, she looked up but soon had look of fear. The Doctor was confused for a second and looked at her direction and instantly got up, she felt her hair on her sides and knew her hair was down, it was probably all over the place and she had to brush it later.

Yep. Being a Time Lady is going to fun.

Clara stood behind her as The Doctor fished out her Sonic Screwdriver and aimed it at the 2 Cybermen who were standing at attention and were standing near the Console. She didn't have the time to see if it still worked because she hadn't used it since she had Regenerated.

"Alright, you may or may not know who I am. I had a long day and had it up to here with all the death, and the end of the world. Leave now or face the wrath of the one… the only… Oncoming Storm." The Doctor said coldly and said the last part for dramatic purposes while protecting Clara.

Clara was taken by surprise by how cold the Doctor's voice was, her old Doctor was the same but this Doctor was a new story, considering she had just Regenerated and she still had a lot to learn about her new Doctor.

"Hmm, redecorated and now looks like me with a cool outfit. Reminds me when I saw a future version of myself and we flirted with each other." The one on the left said, which sounded like an amused voice.

"Yeah, not to mention we've only been alive again for who knows how long and she's already combat ready and about to strike like old times." The one on the right said which sounded like an amused voice with a hint of fear.

"Doctor, what's going on?" Clara asked confused.

The Doctor scanned them and said," Both of them died in their 80's and were probably in a cemetery for a while. Also they somehow fought off the Conversion Process and kept their humanity and were strong willed to do it, so few have done that and I'm one of them. Granted I had a split personality when that happened." The Doctor said.

"Not the fondest memory." Clara said.

"Seems like we missed out on some things." The one on the right said and crossed it's arms.

"If you want me to save you, I'm sorry, I can't. But who are you and how did you manage to fight off the Conversion process?" The Doctor asked with a mix of sympathy and curiosity.

But on the inside she felt she knew these two and hoped she was wrong on who she thought they were.

The two Cybermen looked at each other and sighed, which amused the Doctor a bit.

"That dense as always. Huh Doctor?" The left one said.

"Yep that's our son or daughter-in-law." The other said.

The Doctor thought for a second and her eyes widened, she knew who they were and she was in total shock and didn't want to believe it.

"Rory… Amy?" She said shakily.

The one on the right took a step and said," Hello… Raggedy Man."

* * *

 **That's the end for this chapter. Yep, Amy and Rory are back, but as Cybermen. What will the Doctor do and how will she help? Next chapter soon and coming to the end soon as well. I had finished this chapter during my free time at school and copied it at home.**

 **[1] In the episode Missy also said Belgian's but when I was writing this chapter, the Belgium Bombings happened and so I left that part out, out of respect.**

 **Comment, fav, follow!**


	6. Chapter 5: Finest Hour

**Next chapter is up! This will an exciting and emotional chapter with a throwback to some things.**

 **You have been warned.**

 **I own nothing Doctor Who related and I don't own the Disney references.**

* * *

 **Chapter 5**

Clara didn't know how to help the Doctor. She couldn't comprehend how she was feeling seeing previous companions, who she was very close to and now had the face of one of them, were now Cybermen. Clara vaguely remembered them when she jumped into the Doctor's Time stream and saw glimpses of them and when the TARDIS showed her previous people who had traveled with the Doctor.

She saw The Doctor shaking and tears were glossing her eyes.

The Doctor walked closer to them and felt her hearts cracked a little. And felt the guilt of when they were first sent back by the Weeping Angel and that was the last time she saw them. But now, now she was seeing them as Cybermen, not cold and emotionless ones but one of the few who had fought the Conversion process.

"P-Pond's how… I'm sorry you had to go through this. I will find a way to fix this. I swear." The Doctor said shakily but Clara detected a hint of hatred.

"Doctor… we missed you. And you can't, we know this process is permanent." Cyber-Amy said in her mechanical voice.

"But, that doesn't mean we won't help you end this. Also, why do you have my wife's face?" Cyber-Rory asked with a hint of jealousy in the mechanical voice.

"Don't talk, I can't listen to you, not like this. Here you go." The Doctor said and activated her Sonic at them.

"Try it now." The Doctor said in a neutral voice.

"I will sock this Master or Missy person until she's catatonic." Cyber-Amy said in in her regular voice, but was filled with anger that sent shivers of fear down The Doctor's back.

 _"_ _Yep, same old Amy, terrifying as ever."_ The Doctor thought.

"Sounds better, and the reason I have Amelia's face is because I saw a hallucination of her before I Regenerated and I guess that's how I ended up like this." The Doctor said and stuffed her hands into her Jacket pockets.

"Makes sense, but I got to say, I look good in that outfit." Cyber-Amy said with twinge of Jealousy.

"I actually took some of your clothes from the wardrobe." The Doctor said sheepishly.

"I won't need them anyway. So… what's the plan?"

"Right then, only way to take out a Cyberman is to create an Transient Electromagnetic Disturbance big enough to cover the whole world and take them all out at once. But I'm not going to do that because it will take out all power from everywhere and won't be controlled and it will destroy their Emotion Inhibitor's."

"But is there a way to take out the chips without doing that? And what about the clouds outside?" Cyber-Amy said.

"There is, but I'm not doing that either." The Doctor refused.

"Why can't we use that one? Explain Doctor." Cyber-Amy said.

"Yeah, we know what happens when you do it because you told us. What's the problem?" Cyber-Rory asked.

The Doctor gave them a serious look and said," I'm not going to do it with you two like this. Your chips may be off but you will still perish as well, I will not let that happen again and I will have to live with that guilt forever, I have your face Amy and it's a constant reminder of what I could have done but wasn't able to do for you two… the same goes for Katarina, Sara, Adric, Kamelion and probably others in the future. I will… find a way."

Clara walked over to The Doctor and enveloped her in a hug trying to comfort her for everything she had been through for the past 1,000+ years. Her previous Doctor wasn't as emotional or open as this one but she had to get used to it.

The Doctor didn't cry but relaxed and felt two metal hands on her shoulders and jumped a little. She wasn't used to being this close to Cybermen without them trying to kill her, even thought the ones she was with were her former companions and family.

"At least you found someone when I told you and if you didn't, then there would have been hell to pay and you would have had a beating of a lifetime Raggedy Girl." Cyber-Amy said in a joking manner but the Doctor knew there was some seriousness in it.

"Plus, our time was over when the Angels touched us, this is our last time with you Doctor and we hope you move forward." Cyber-Rory said.

"Right let's go outside and see what's going on. Also play your part." The Doctor said.

They walked outside to find themselves in a cemetery surrounded by newly formed Cybermen.

"So do you know what Missy's plan is?" The Doctor asked.

"Well, we can tell those clouds will rain down pollen again and probably turn everyone else into Cybermen." Cyber-Rory said.

"Do you know if it can be stopped?" Clara asked.

"We don't know." Cyber-Amy said unsure.

A sound came nearby and they all looked at blue energy where Missy teleported and floated down a little to the ground with an umbrella like she was an evil version of Mary Poppins.

"Well did you see that, quite an entrance if do say so myself. Doctor if you want grieve do it later we have business." She said not caring.

Cyber-Amy clenched her fists and wanted to badly to shoot her but The Doctor would want her alive so she can figure out how to stop all of this.

"What is your game?" The Doctor said with venom dripping from her voice.

"Oh well now, aren't we using our angry voices? I might have to reconsider giving you your gift." Missy said in a fake hurt tone.

"What gift?"

Missy held a bracelet that looked like a communicator and said," Cyber dears look at Mommy. Hand up and down, bring up the right and then lower it and do the robot a little."

As she said that the Cybermen did as they were commanded, except for Amy and Rory.

"You see the Doctor the power is all in the wrist, you just have to know how to use it and they will do exactly what they say. Now, every man, woman and child are now at my command. An indestructible Army that can take over planets, with that the more they kill the more they recruit into their numbers. Happy birthday."

Clara gave the Doctor a confused look. She didn't know it was her birthday and if she had known then she would have had done something for her. While The Doctor didn't notice but was in thought and confused.

"You didn't know did you? It's lucky one of us remembers these things. Not even your friend their knows. But any way, Happy Birthday." Missy said and handed The Doctor her controller bracelet and put it on her wrist.

"Mrs. President." She said in small singing voice and did a curtsy.

"Doctor." The Cybermen said, marched in place and had their heads bowed except Cyber-Amy and Cyber-Rory.

"Tiny bit pleased?"

The Doctor looked around confused while Missy rolled her eyes.

"C'mon crack a smile why don't ya? This one seems to scowl, be stubborn and get angry a lot."

"Why are you doing this? Just to give me an Army?" The Doctor said with a scowl.

"Well I don't need one do I? No one knows more about being right more but you."

The Doctor was about to take off the controller but Missy stopped her.

"Give a good girl fire cover and they won't run out of people to kill."

"I don't want an Army!"

"Oh now that's the trouble! Yes you do and you always wanted one! All those people suffering in the Dalek camps, all the people you couldn't save or could save, now you can save them!"

The Doctor had her arms crossed thinking of what to do. Clara had had a scowl of what's going but she heard the clenching of fists behind her and assumed Cyber-Amy and Cyber-Rory were doing it out of anger and disbelief.

"The bad guys always win and for once the good guys win it all!" She mockingly with her fist raised up.

"No one, could have that kind of power."

"Not just no one but you of course Doctor. And you don't have a choice there's only one way of not letting these storm clouds rain down and killing all of these Monkeys you love so much. Go and conquer the Universe Mrs. President!"

"Show another bad girl how it's done." Missy said and bowed to the ground.

The Doctor got frustrated, tore off the bracelet and said," Why ae you doing this?!"

"I need to let you know we're not so different… I need my friend back." She said sincerely while The Doctor looked skeptical.

"Every battle, every war, every conflict, every nation… for now on you decide the outcome and as an added bonus you can save all those you have met and stop them from dying as well."

The Doctor looked down and still in thought and Missy continued.

"From now on you decide the outcome. What's the Mrs. President? Don't you trust yourself?"

The Doctor started more and had flashbacks of all the time she failed.

* * *

 _T_ _he 5_ _th_ _Doctor, Nyssa and Tegan watch helplessly as Adric dies when the ship crashes into the earth._

 _"_ _Now I'll never know if I was right."_

 _10_ _th_ _Doctor holds his daughter Jenny as she lays dying after she takes the bullet from General Cobb that was meant for The Doctor._

 _"_ _You need to hold on… you need to, you hear me? We got things to do, you hear me." He said emotionally._

 _"_ _Sounds good." Jenny said, trying to sound confident._

 _Not being able to save River when she perished in the library._

 _"_ _You and me time and space and you would just run." River said emotionally._

 _The 10_ _th_ _Doctor about to erasing the mind of Donna so she won't burn._

 _"_ _Oh My God. You can't make me go back Doctor please!" Donna said, tears in her eyes._

 _"_ _Donna… Donna Noble. I'm so, so sorry." The Doctor said with tears as well." But, we had the best of times. Goodbye." He said and placed his hands on her temples._

 _"_ _No, no, no, no!" She said before she fell unconscious._

 _11_ _th_ _Doctor tries to talk Amy out of being touched by a Weeping Angel to be with Rory._

 _"_ _You are creating a fixed time, and I won't be able to see you again." The Doctor said near tears._

 _"_ _I'll be fine." Amy said in tears._

 _"_ _Amy Please, just come back into the TARDIS."_

 _"_ _[Sniffs]… Raggedy Man… Goodbye." She said and vanishes leaving the Doctor devastated._

* * *

The Doctor looked at Cyber-Amy and Cyber-Rory who were looking down and she knew they were thinking about what they did to the Doctor and she forgave again for what they had done. Clara was close to having tears that made the Doctor's Heart's break.

The Doctor found her conclusion and got to eye level with Missy.

"Thank you, thank you so much." The Doctor said and hugged Missy.

"I wasn't sure, I can't decided from time to time, and now I know." She said and got up.

"I am not a good person nor a bad person, not a General or a President nor a God of any of any sorts. I can't save anyone."

"I am an idiot." She said with a smile.

Clara gave her a confused look, Cyber-Amy and Cyber-Rory looked at each other what could have been read as confusion as well. While Missy gave her a look as well.

"With a box, a screwdriver, just passing through. Helping out the best I can and learning, just not about new things but mistakes. I thought I got this face for not saving everyone and this was a curse but I was wrong. This means I can't save everyone but will try my hardest to save and protect them. Especially her over there and Amy and Rory. Amy catch!" The Doctor said and threw the bracelet at Cyber-Amy.

She caught it and strapped it on her wrist.

"You didn't notice did you? Two of your own soldier's not obeying because they fought it and their humanity stayed." The Doctor gloated with a smile.

"No that's wrong that's not possible." Missy said in disbelief and looked at Cyber-Amy.

Cyber-Amy walked over to Missy with Rory and said," Sorry to rain on your parade but the rain is not going to fall anytime soon." She said with authority.

"Oh? And why won't it?"

"Because they will burn and won't harm anyone else." Cyber-Rory said.

"And who will?" Missy said with a raised eyebrow and her hands on her hips.

"We will of course." Cyber-Amy said.

"Two Cybermen won't be enough to save the planet."

"Correct." Cyber-Rory said and got the bracelet from Cyber-Amy.

"Attention! Alright, I'm not good at this speech stuff but we know this is all bad. We will save everyone! Not as some group of emotionless killing machines but as individuals and we won't mope around feeling sorry for ourselves!" He said and handed the bracelet to his wife.

"Could've started off better. You will take orders from us and not from a raving lunatic who dresses like a an evil Disney character!"

"Excuse me?" Missy said offended but Cyber-Amy ignored her.

Both turned around to the Doctor with Cyber-Amy saying." Raggedy Girl, Clara, take care of yourselves and move on. We're done our part and we'll be leaving."

"And know the both of us love you and River. Tell her that, tell my dad and tell her parents. Goodbye."

The Doctor nodded with a sad smile and said," Run along Ponds. Go and save this planet."

Cyber-Amy and Cyber-Rory nodded at each other. They hit their chest plates to activate their rockets and held each other's hand and flew off with all the other Cybermen into the clouds. They exploded a second later with the clouds disappearing and the day becoming bright. The same was happening all over the world.

 _"_ _Goodbye Ponds."_ She thought and a single tear fell.

"Well, all the clouds are gone." Clara said.

"Yes, thank you Captain Obvious." The Doctor said with a smile while Clara narrowed her eyes at her.

"Burnt up. Totally burned. Burnt to nothing." She said.

"I'm sorry." Clara said.

"10-0-11-0-0 by 0-2." Missy said.

"What did you say?" The Doctor asked.

Missy had a neutral expression said," Coordinates for Gallifrey, right where it was and you didn't think to look."

"You are lying." The Doctor said getting angry.

"We can… we can go together just like the old days?"

"You'll be clamped in irons."

"If you like."

"Doctor, I assume you'll remember those coordinates?" Clara asked and had Missy's device in her hands and pointed it at Missy.

"Don't, don't you dare Clara." The Doctor said.

"Doctor, you've been through a lot today and I'm trying to help."

"Clara don't, I won't let you do this. Let me." The Doctor said and the device.

"Ooo, getting a little low now are we. Might as well ask you to say something nice Doctor." Missy said and leaned on a gravestone.

The Doctor rubbed her face, aimed at her but a blue beam consumed Missy and she disappeared. The Doctor and Clara had a look of confusion and turned around. A lone Cyberman lowered its weapon and pointed at an area down the hill.

Clara looked and her eyes widened.

"Doctor look!" She said and took off.

They both went to the bottom of the hill to find Kate lying on the ground unconscious. And The Doctor got down and checked her to see if she was alright.

"Kate, she's still breathing. But she can't be alive at all, she fell out a plane." The Doctor said in confusion.

"Well she's here." Clara said.

The Doctor's eyes widened, looked up the hill and said," I think it has to do with the Cyberman."

"Doctor, she's talking about her Dad." Clara said.

The Doctor looked at Clara and back at the Cybermen version of Brigadier Alistair Gordon Lethbridge-Stewart with a knowing grin.

"Of course, Earth's darkest hour and mine. Where else would you be old friend?" She said with a fond smile.

The Doctor did something she should had done a long time ago. She saluted the Brigadier and he nodded and soon flew away into the distance with The Doctor and Clara looking on.

* * *

 **And that the end of this Chapter. One more left until I'm finished. I would like to thank everyone who has reviewed whom I will name next chapter. I almost cried while writing this. I had to look up Companion deaths and their departures. I will do the end like Deep Breath and Death in heaven. It might be short a chapter so I might have it up later.**

 **P.S. Sorry in advance if I didn't add other character's to the list of dead companions. I considered putting in Rose but she lived and I thought about Peri but she ended up living in a different way but you'll have to look it up yourselves.**

 **Thanks and see you all later!**


	7. Chapter 6: Phone Call

**Last Chapter! Special thanks to TimeLordPrime, dudelove85, and Beware the Weeping Angels for commenting and giving me advice.**

 **I don't own anything. Especially the Forrest Gump quote.**

 **Enjoy!**

* * *

 **Chapter 6**

The TARDIS materialized into Clara's flat, in her Living room.

Before that they had gotten Kate back to UNIT to get her checked out, talked to Brian and Amy's Parents about what Amy and Rory had said and done. Although it was difficult for Amy's parents because she had to explain Regeneration to them and tell them what had happened and she was half suspecting Amy's mom would have slapped her like all the mother's she had met, which had started with Rose's mother, but she didn't.

The Doctor was standing at the console deep in thought about the day and how she had Regenerated, dealt with her feelings, had to stop by the end of the world that was orchestrated by an old enemy/friend, caught up with her closes Companions/family and made peace with them.

Clara hadn't left yet; she was probably thinking of everything that has happened as well. Clara had been a huge help with everything. She probably had River to thank for that because if Clara wasn't there then she didn't know what she would have done with dealing with her Regeneration.

She found a hair band that the TARDIS gave her and put her hair back into a Ponytail, she had thought about cutting it but she wanted to keep it the same, just like Amy would.

She soon heard a buzzing coming from somewhere but didn't know what it was and it started to become irritating but Clara said she would be right back to take a call and The Doctor smiled, she knew who it was.

Clara walked out of the TARDIS, phone in hand, and sat on her couch.

"Hello?" Clara asked.

"Hello… it's me." A familiar raspy voice said on the other line and Clara could tell he was breathing heavily. **[1]**

"Yes it's you, who is this?" She asked in confusion.

"It's me Clara… The Doctor."

Clara eyes widened and said,"… What do you mean the Doctor?" Clara asked, starting to get emotional.

The 11th Doctor was sitting in the TARDIS, feeling wrecked and knew he was Regenerating soon but had to call Clara so he could help her when he did.

"I'm phoning you from Trenzalore."

"I don't-"

"Before I change, buts it a' coming, oh it's a' coming. Not long now… oh I can feel it."

Clara put the phone on her chest and tried to hold back tears and kept her composure. She put the phone to her ear again and listened.

"[sniff]… Why? Why did you do this?"

"Because, I think this one's going to be a whopper. When a Time Lord Regenerates… it's a lottery, or a box of chocolates, you don't know what you're going to get."

"She's great so far and different but also emotional." Clara said, wanting to hear the reaction.

The line was silent for a second and repeated what River had said earlier," Well…first time for everything I suppose."

Clara let out a small emotional laugh and The Doctor continued," I know you might be scared Clara… but I know she will be too, she will need someone to help her through it… and I know you can do it. Promise me that."

"I promise." Clara said and wiped a tear from her face.

The 12th Doctor walked out of the TARDIS, leaned on the door with her hands in her pockets and said," So, who is it? Is that the Doctor?" the Doctor asked, with a ghost of a grin.

"Yes." She said to the 12th.

"Oh, I sound Scottish, and I hope I'm Ginger and still young… but don't tell me… I want to be surprised." The 11th Doctor on the phone said with a hint of excitement.

Clara giggled a little and said," Don't worry I won't, and I promise you to be by your side every step of the way." Clara said with a sad smile.

"Thank you Clara, remember, don't be afraid and help her through this… My Impossible Girl."

"I will Doctor and… your welcome."

The line went dead. Clara wiped a couple of tears from her face and saw The Doctor was standing near her with her hands stuffed in her pockets.

"So, what did he say? Will you help me?" She asked.

Clara smiled a little and said," It's not nice to eavesdrop."

The Doctor chuckled and said," It's me Clara, you know that. Not on the phone, not wearing a ridiculous outfit but I'm here standing here. I know you've been through a lot today and you've seen a new side of me. All I ask, as a friend, is to put that behind us and continue on." She said.

Clara looked at The Doctor and studied her, which was awkward for her. Clara smiled and hugged her and she gave one back.

"I know it's you Ginger Girl." She said.

"C'mon you want to stay here or head to a nice planet? I know one that has the biggest Amusement Park you will ever see."

"Actually, can we go to Gallifrey and show me around, I don't know if Missy was telling the truth but it can't hurt to check."

The Doctor smirked and said," Alright let's go. I'll let you meet Romana, Leela and both K-9's."

The Doctor and Clara walked into the TARDIS, Clara sat in the Captains chair while The Doctor was going to set the Coordinates for Gallifrey. But another ringing soon came and it was the TARDIS phone.

The Doctor turned around and saw the phone was now on the inside instead of the outside.

"Thank you Sexy." She said and went to the phone.

She pressed the phone to her hear and said," Hello, this is the Doctor."

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 **And that's it. I know cliffhanger. Hahahahahaha! The rest will be in the sequel I will plan soon. I hoped everyone liked this and please check out my other fics.**

 **[1] I know what some of you were thinking. That was part of the dialogue in Deep Breath and I didn't do an Adele reference.**

 **Thunderstrike16 signing off!**


	8. Revision Notice

**After going over the story, I've noticed some mistakes and other things that have to do with this story. Granted, I was still new to writing and posting on this site when I first published this. So I decided to make a revised version of this, the original will stay and I won't take it down. The start of the Revised 'Amy Pond: The 12th Doctor' will start soon, maybe during Christmas break or early next near. Hope you guys like it when I publish the first chapter and thanks for all the support I've gotten since the beginning the year when I published my first fanfic on this site.**

 **Also for The Doctor Amy: The Beginning, I'm not sure if I will revise it, considering I'm still writing it.**

 **I also ask you all to check out my other stories as well to see what you all think. Comments, suggests and feedback are welcomed.**

 **-Thunderstrike16**


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